My workflow for generating the kindle books is as follows:
1) Use indesign
2) use sigil to tweak the epub
3) use kindle previewer to get mobi.

Now the issue is, I get a double cover on all my kindle books. I tried every solution available on net including the setting linear=no in the content.opf file.

Could anyone help me how to stop these double covers from occurring?

Remove your cover.html file, which I'm assuming you have, or some html file that contains nothing but the cover image. Leave your cover image in the /Images folder. Tag the actual cover image with "cover" semantics, and ensure that the cover image is also correctly identified as same in the OPF. Drop the file on KP. (Have you tried this already? You mentioned that you tried linear=no, which is not the same thing as removing the html file that encloses the cover, but did you try this?)

That should solve your issue. I've actually had ePUBs with the cover.html file work fine, but I'm guessing that INDD does something else withe the cover.html file that somehow, precludes it from working. We use INDD for print, but I would never use it to make an ebook if it did not have a print component; causes more work than it saves.